If your employer requires that you still submit an expense report with receipts for your travel expenses, then the per diem travel allowance is not taxable income to you.
If your employer does not require expense reports and receipts, then this allowance would be included in your taxable income.
If it turns out that you are requried to include this in your taxable income, then you can fill out Form 2106 for Unreimbursed Employee Expenses as part of your tax return and claim your actual travel expenses on that form as part of your itemized deductions.
Here is a link to an IRS publication which explains some of the more frequently asked questions about per diem allowances.
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